I'm trying to install Ubuntu from a bootable USB drive. If I run Ubuntu from the drive, I can successfully mount both of my physical drives:

Drive 1 is in 3 partitions: 8GB for recovery, 400GB for Windows 8 install, 550GB empty partition formatted to NTFS
Drive 2 is in one single 500GB partition formatted to NTFS and used for media storage

All files are accessible and things run as expected. When I try to install Ubuntu, however, and choose the option to "Install side by side with Windows 8", the installer only lists Drive 2. I really want to install the OS to the empty partition on Drive 1. Beyond going into the "Something Else" option and manually selecting to install the OS to the partition (it sees it there) and then hopefully putting the bootloader on the right partition, is there a way to get the automatic method to detect my drive appropriately?

I'm not exactly sure why Ubuntu would not properly detect your disk with Windows 8 for the "side by side" install target, but it may have something to do with your partitioning scheme. The Ubuntu Installer would normally resize the Windows partition to make free space, then create two new partitions (one formatted as EXT4 and the other formatted as swap) to install Ubuntu on. Since your partitioning scheme is more complicated than that of the typical Windows installation, its possible that the Ubuntu Installer is not suggesting your primary disk as an install target because it doesn't know how to deal with the existing partitions.

Assuming my analysis of the situation is correct, you can probably solve the problem without too much trouble. Use GParted (which is installed on all Ubuntu live discs) to delete the 550 GB NTFS partition on your primary drive. Next start the Ubuntu Installer and navigate to the main partitioning screen. Select the "use largest available free space" option and your disk should be partitioned as intended.